Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

Abstract

Summary Negativicutes are gram‐negative bacteria characterized by two cell membranes, but they are phylogenetically a side‐branch of gram‐positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram‐negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co‐evolved vertically with their hosts and thus resemble gram‐positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram‐negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu‐like candidate prophage and no clear P2‐like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence‐related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross‐order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co‐evolution despite horizontal phage mobilization.

Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae

“…To comprehensively examine the association of each prophage WO variant with its chromosomal location in Wolbachia , we mapped integration sites, determined by the recombinase or the most 5’- WO gene, on the chromosome with respect to normalized distance from the putative origin of replication, ori [ 61 ]. There is a clustering of prophage WO insertion loci, particularly sr3WO, opposite the putative origin of replication ( Fig 3B ; Chi-square 2-tailed, p = 0.0035) that is similar to the localization patterns of temperate phages in Escherichia , Salmonella , and Negativicutes [ 62 – 65 ]. WO chromosomal location patterns support a model in which prophage insertions and WO-like Islands may not be tolerated in certain regions of the Wolbachia chromosome, in this case the region directly surrounding the predicted origin of replication.…”

Metabolomic and metagenomic analyses of the Chinese mitten crab Eriocheir sinensis after challenge with Metschnikowia bicuspidata

“…They are widely distributed in nature and exist in anaerobic habitats, such as aquatic sediment, soil, anaerobic sewage digesters, and animal gastrointestinal tracts. Similarly, Rhodocyclales and Acidaminococcales are also adapted for anaerobic environments (Rands et al, 2019;Wang et al, 2020). These findings indicated that M. bicuspidata infection significantly At the genus level, 37 genera increased significantly, and 21 genera belonged to the phylum Firmicutes, of which 11 genera belonged to the order Eubacteriales, including Hespellia, Acetivibrio, Lachnoanaerobaculum, Youngiibacter, Defluviitalea, Proteocatella, Anaeromassilibacillus, Asaccharospora, Anaerotruncus, Geosporobacter, and Anaerotignum.…”